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From: Traci Clymer (clymert_at_duq.edu)
Date: Fri Jun 22 2012 - 09:13:36 CDT

I am trying to use psfgen to generate a psf file for bicarbonate. It creates the files but they are empty. I think the problem is with my topology file but I'm not sure exactly what it is. Any help would be greatly appreciated!

This is the output I get from the TK console and I have attached my topology, pdb, and pgn files

MASS 1 C 12.01000 !C 12.01 0.616 sp2 C carbonyl group
MASS 2 CA 12.01000 !CA 12.01 0.360 sp2 C pure aromatic (benzene)
MASS 3 CB 12.01000 !CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring junction
MASS 4 CC 12.01000 !CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS
MASS 5 CD 12.01000 !CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C
MASS 6 CK 12.01000 !CK 12.01 0.360 sp2 C 5 memb.ring in purines
MASS 7 CM 12.01000 !CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6
MASS 8 CN 12.01000 !CN 12.01 0.360 sp2 C aromatic 5&6 memb.ring junct.(TRP)
MASS 9 CQ 12.01000 !CQ 12.01 0.360 sp2 C in 5 mem.ring of purines between 2 N
MASS 10 CR 12.01000 !CR 12.01 0.360 sp2 arom as CQ but in HIS
MASS 11 CT 12.01000 !CT 12.01 0.878 sp3 aliphatic C
MASS 12 CV 12.01000 !CV 12.01 0.360 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
MASS 13 CW 12.01000 !CW 12.01 0.360 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
MASS 14 CS 12.01000 !C* 12.01 0.360 sp2 arom. 5 memb.ring w/1 subst. (TRP)
MASS 15 CY 12.01000 !CY 12.01 0.360 nitrile C (Howard et al.JCC,16,243,1995)
MASS 16 CZ 12.01000 !CZ 12.01 0.360 sp C (Howard et al.JCC,16,243,1995)
MASS 17 H 1.00800 !H 1.008 0.161 H bonded to nitrogen atoms
MASS 18 HC 1.00800 !HC 1.008 0.135 H aliph. bond. to C without electrwd.group
MASS 19 H1 1.00800 !H1 1.008 0.135 H aliph. bond. to C with 1 electrwd. group
MASS 20 H2 1.00800 !H2 1.008 0.135 H aliph. bond. to C with 2 electrwd.groups
MASS 21 H3 1.00800 !H3 1.008 0.135 H aliph. bond. to C with 3 eletrwd.groups
MASS 22 HA 1.00800 !HA 1.008 0.167 H arom. bond. to C without elctrwd. groups
MASS 23 H4 1.00800 !H4 1.008 0.167 H arom. bond. to C with 1 electrwd. group
MASS 24 H5 1.00800 !H5 1.008 0.167 H arom.at C with 2 elctrwd. gr,+HCOO group
MASS 25 HO 1.00800 !HO 1.008 0.135 hydroxyl group
MASS 26 HS 1.00800 !HS 1.008 0.135 hydrogen bonded to sulphur (pol?)
MASS 27 HW 1.00800 !HW 1.008 0.000 H in TIP3P water
MASS 28 HP 1.00800 !HP 1.008 0.135 H bonded to C next to positively charged gr
MASS 29 HZ 1.00800 !HZ 1.008 0.161 H bond sp C (Howard et al.JCC,16,243,1995)
MASS 30 N 14.01000 !N 14.01 0.530 sp2 nitrogen in amide groups
MASS 31 NA 14.01000 !NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS)
MASS 32 NB 14.01000 !NB 14.01 0.530 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
MASS 33 NC 14.01000 !NC 14.01 0.530 sp2 N in 6 memb.ring w/LP (ADE,GUA)
MASS 34 N2 14.01000 !N2 14.01 0.530 sp2 N in amino groups
MASS 35 N3 14.01000 !N3 14.01 0.530 sp3 N for charged amino groups (Lys, etc)
MASS 36 NT 14.01000 !NT 14.01 0.530 sp3 N for amino groups amino groups
MASS 37 NS 14.01000 !N* 14.01 0.530 sp2 N
MASS 38 NY 14.01000 !NY 14.01 0.530 nitrile N (Howard et al.JCC,16,243,1995)
MASS 39 O 16.00000 !O 16.00 0.434 carbonyl group oxygen
MASS 40 O2 16.00000 !O2 16.00 0.434 carboxyl and phosphate group oxygen
MASS 41 OW 16.00000 !OW 16.00 0.000 oxygen in TIP3P water
MASS 42 OH 16.00000 !OH 16.00 0.465 oxygen in hydroxyl group
MASS 43 OS 16.00000 !OS 16.00 0.465 ether and ester oxygen
MASS 44 P 30.97000 !P 30.97 1.538 phosphate,pol:JACS,112,8543,90,K.J.Miller
MASS 45 S 32.06000 !S 32.06 2.900 S in disulfide linkage,pol:JPC,102,2399,98
MASS 46 SH 32.06000 !SH 32.06 2.900 S in cystine
MASS 47 Zn 65.40000 !Zn 65.4 Zn2+
MASS 48 LP 3.00000 !LP 3.00 0.000 lone pair
MASS 49 CI 12.01000 !CI 12.01 ES: BSC0
MASS 50 Se 78.96000 !Se 78.960 2.900 same as ss ES: from all_modrna08!
MASS 51 SO 32.06000 !SO 32.060 2.900 same as ss ES: from all_modrna08!
MASS 52 SS 32.06000 !SS 32.060 2.900 same as ss ES: from all_modrna08!
MASS 53 IM 35.45000 !IM 35.45 3.235 assumed to be Cl- (ion minus)
MASS 54 IB 131.00000 !IB 131.0 'big ion w/ waters' for vacuum (Na+, 6H2O)
MASS 55 CAL 40.08000 !CAL 40.08 calcium; ES: formerely: C0
MASS 56 CU 63.55000 !CU 63.55 copper
MASS 57 FE 55.00000 !FE 55.00 iron
MASS 58 MG 24.30500 !MG 24.305 0.120 magnesium
MASS 59 Li+ 6.94000 !Li+ 6.94 0.029 lithium pol: J. Phys. Chem. 11,1541,(1978) ES: from ionsjc_tip3p
MASS 60 SOD 22.99000 !SOD 22.99 0.250 sodium pol: J. Phys. Chem. 11,1541,(1978) ES: from ionsjc_tip3p
MASS 61 POT 39.10000 !POT 39.10 1.060 potassium ES: from ionsjc_tip3p
MASS 62 Rb+ 85.47000 !Rb+ 85.47 rubidium ES: from ionsjc_tip3p
MASS 63 ES+ 132.91000 !Cs+ 132.91 cesium ES: from ionsjc_tip3p
MASS 64 F- 19.00000 !F- 19.00 0.320 fluorine ES: from ionsjc_tip3p
MASS 65 CLA 35.45000 !CLA 35.45 1.910 chlorine (Applequist) ES: from ionsjc_tip3p
MASS 66 Br- 79.90000 !Br- 79.90 2.880 bromine (Applequist) ES: from ionsjc_tip3p
MASS 67 I- 126.90000 !I- 126.9 4.690 iodine (Applequist) ES: from ionsjc_tip3p

RESI BCT -1.0000 GROUP ATOM C C 0.996! ATOM O1 O -0.842! ATOM O2 O -0.782! ATOM O3 OH -0.752! ATOM H3 HO 0.379! !END GROUP BOND C O1 ! 1.25974 C O BOND C O2 ! 1.24476 C O BOND C O3 ! 1.45426 C OH BOND O3 H3 ! 0.97327 OH HO IC O1 C O3 H3 1.25974 112.983 -0.019 99.917 0.97327 IC O2 C O3 H3 1.24476 113.872 -179.982 99.917 0.97327 PATCH FIRST NONE LAST NONE
 
END

>Main< (VMD_files) 3 % resetpsf
clearing structure, preserving topology and aliases
>Main< (VMD_files) 4 % source bct.pgn
reading topology file top_bicarb.txt

building segment X
reading residues from pdb file BCT_VMD.pdb
extracted 1 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file BCT_VMD.pdb for segment X
Warning: failed to set coordinate for atom C BCT:107 X
Warning: failed to set coordinate for atom O3 BCT:107 X
Warning: failed to set coordinate for atom O2 BCT:107 X
Warning: failed to set coordinate for atom O1 BCT:107 X
Warning: failed to set coordinate for atom H3 BCT:107 X
Info: guessing coordinates for 0 atoms (0 non-hydrogen)
Info: writing pdb file BCT1.pdb
Info: pdb file complete.
Info: writing psf file BCT1.psf
total of 0 atoms
total of 0 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
total of 0 cross-terms
Info: psf file complete.
>Main< (VMD_files) 5 %

  • application/octet-stream attachment: bct.pgn