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标题: 求助：对核酸体系进行分子动力学模拟出现问题 [打印本页]

作者
Author: 木月十七岁 时间: 2025-11-14 21:07
标题: 求助：对核酸体系进行分子动力学模拟出现问题
各位老师好，我使用gmx对核酸体系进行分子动力学模拟，第一步gmx pdb2gmx -f input.pdb -o output.gro -p topol.top -ter 使用charmm36力场和tip3p水，出现下面情况。（附件有核酸的pdb文件）

Back Off! I just backed up topol.top to ./#topol.top.1#Processing chain 1 (21930 atoms, 1021 residues)
Identified residue U744 as a starting terminus.
Identified residue C2767 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for U-744
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
6
Start terminus U-744: 5PHO
Select end terminus type for C-2767
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
6
End terminus C-2767: 3TER
Opening force field file E:\APPS_20251010\gmx2019.6_GPU/share/gromacs/top/charmm36-jul2022.ff/aminoacids.arn
Opening force field file E:\APPS_20251010\gmx2019.6_GPU/share/gromacs/top/charmm36-jul2022.ff/na.arn

-------------------------------------------------------
Program: gmx pdb2gmx, version 2019.6
Source file: src\gromacs\gmxpreprocess\pdb2gmx.cpp (line 745)

Fatal error:
Atom OP1 in residue U 744 was not found in rtp entry URA with 32 atoms
while sorting atoms.
.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

作者
Author: sobereva 时间: 2025-11-15 06:56
参考北京科音分子动力学与GROMACS培训班（http://www.keinsci.com/KGMX）幻灯片：
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